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 9NV3 | pdb_00009nv3

Hybrid model of a complex of BREX proteins BrxB and PglZ from Salmonella typhimurium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9NV3

This is version 1.1 of the entry. See complete history. 

Literature

PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB.

Readshaw, J.J., Doyle, L.A., Puiu, M., Kelly, A., Nelson, A., Kaiser, A.J., McGuire, S.F., Peralta Acosta, J., Smith, D.L., Stoddard, B.L., Kaiser, B.K., Blower, T.R.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf540
  • Primary Citation Related Structures: 
    9NV3

  • PubMed Abstract: 

    BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly diverse group of phage defence systems found throughout bacteria and archaea. The varied BREX Types harbour multiple protein subunits (between four and eight) and all encode a conserved putative phosphatase, PglZ, and an equally conserved, putative ATPase, BrxC. Almost all BREX systems also contain a site-specific methyltransferase, PglX. Despite having determined the structure and fundamental biophysical and biochemical behaviours of several BREX factors (including the PglX methyltransferase, the BrxL effector, the BrxA DNA-binding protein, and a commonly-associated transcriptional regulator, BrxR), the mechanism by which BREX impedes phage replication remains largely undetermined. In this study, we identified a stable BREX sub-complex of PglZ:BrxB, generated and validated a structural model of that protein complex, and assessed the biochemical activity of PglZ from BREX, revealing it to be a metal-dependent nuclease. PglZ can cleave cyclic oligonucleotides, linear oligonucleotides, plasmid DNA and both non-modified and modified linear phage genomes. PglZ nuclease activity has no obvious role in BREX-dependent methylation, but does contribute to BREX phage defence. BrxB binding does not impact PglZ nuclease activity. These data contribute to our growing understanding of BREX phage defence.


  • Organizational Affiliation: 
    • Department of Biosciences, Durham University, Stockton Road, DurhamDH1 3LE, UK.

Macromolecule Content 

  • Total Structure Weight: 125.53 kDa 
  • Atom Count: 8,684 
  • Modeled Residue Count: 1,065 
  • Deposited Residue Count: 1,086 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DUF1788 domain-containing protein199Salmonella enterica subsp. enterica serovar Typhimurium str. D23580Mutation(s): 0 
Gene Names: STMMW_44421
UniProt
Find proteins for A0A6C7ILK3 (Salmonella typhimurium (strain D23580))
Explore A0A6C7ILK3 
Go to UniProtKB:  A0A6C7ILK3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6C7ILK3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PglZ domain-containing proteinB [auth C]887Salmonella enterica subsp. enterica serovar Typhimurium str. D23580Mutation(s): 0 
Gene Names: STMMW_44371
UniProt
Find proteins for A0A6C7IK08 (Salmonella typhimurium (strain D23580))
Explore A0A6C7IK08 
Go to UniProtKB:  A0A6C7IK08
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6C7IK08
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/Y003659/1
The Lister Institute of Preventive MedicineUnited Kingdom--
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T008695/1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R35GM148166
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140375
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5 P30 CA015704-49
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Data collection, Database references